karyoploteR

DOI: 10.18129/B9.bioc.karyoploteR    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see karyoploteR.

Plot customizable linear genomes displaying arbitrary data

Bioconductor version: 3.11

karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

Author: Bernat Gel <bgel at igtp.cat>

Maintainer: Bernat Gel <bgel at igtp.cat>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("karyoploteR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("karyoploteR")

 

HTML	R Script	karyoploteR vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, CopyNumberVariation, Coverage, DNASeq, DataImport, MethylSeq, OneChannel, Sequencing, Software, Visualization
Version	1.14.1
In Bioconductor since	BioC 3.5 (R-3.4) (3.5 years)
License	Artistic-2.0
Depends	R (>= 3.4), regioneR, GenomicRanges, methods
Imports	regioneR, GenomicRanges, IRanges, Rsamtools, stats, graphics, memoise, rtracklayer, GenomeInfoDb, S4Vectors, biovizBase, digest, bezier, GenomicFeatures, bamsignals, AnnotationDbi, grDevices, VariantAnnotation
LinkingTo
Suggests	BiocStyle, knitr, testthat, magrittr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Hs.eg.db, org.Mm.eg.db, pasillaBamSubset
SystemRequirements
Enhances
URL	https://github.com/bernatgel/karyoploteR
BugReports	https://github.com/bernatgel/karyoploteR/issues
Depends On Me	CopyNumberPlots
Imports Me	CNVfilteR
Suggests Me	Category
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	karyoploteR_1.14.1.tar.gz
Windows Binary	karyoploteR_1.14.1.zip
macOS 10.13 (High Sierra)	karyoploteR_1.14.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/karyoploteR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/karyoploteR
Package Short Url	https://bioconductor.org/packages/karyoploteR/
Package Downloads Report	Download Stats